hh_psc_alpha.h

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/*
 *  hh_psc_alpha.h
 *
 *  This file is part of NEST.
 *
 *  Copyright (C) 2004 The NEST Initiative
 *
 *  NEST is free software: you can redistribute it and/or modify
 *  it under the terms of the GNU General Public License as published by
 *  the Free Software Foundation, either version 2 of the License, or
 *  (at your option) any later version.
 *
 *  NEST is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 *
 */
 
#ifndef HH_PSC_ALPHA_H
#define HH_PSC_ALPHA_H
 
// Generated includes:
#include "config.h"
 
#ifdef HAVE_GSL
 
// External includes:
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_odeiv.h>
#include <gsl/gsl_sf_exp.h>
 
// Includes from nestkernel:
#include "archiving_node.h"
#include "connection.h"
#include "event.h"
#include "nest_types.h"
#include "recordables_map.h"
#include "ring_buffer.h"
#include "universal_data_logger.h"
 
namespace nest
{
extern "C" int hh_psc_alpha_dynamics( double, const double*, double*, void* );
 
// clang-format off
/* BeginUserDocs: neuron, Hodgkin-Huxley, current-based, soft threshold
 
Short description
+++++++++++++++++
 
Hodgkin-Huxley neuron model
 
Description
+++++++++++
 
``hh_psc_alpha`` is an implementation of a spiking neuron using the Hodgkin-Huxley
formalism.
 
1. Postsynaptic currents
Incoming spike events induce a postsynaptic change of current modelled
by an alpha function. The alpha function is normalized such that an event of
weight 1.0 results in a peak current of 1 pA.
 
 
2. Spike Detection
Spike detection is done by a combined threshold-and-local-maximum search: if
there is a local maximum above a certain threshold of the membrane potential,
it is considered a spike.
 
See also :footcite:p:`Gerstner2002`, :footcite:p:`Dayan2001`, :footcite:p:`Hodgkin1952`.
 
For details on asynchronicity in spike and firing events with Hodgkin Huxley models
see :ref:`here <hh_details>`.
 
Parameters
++++++++++
 
The following parameters can be set in the status Dictionary.
 
========  ======  ============================================================
V_m       mV      Membrane potential
E_L       mV      Leak reversal potential
C_m       pF      Capacity of the membrane
t_ref     ms      Duration of refractory period
g_L       nS      Leak conductance
tau_ex    ms      Rise time of the excitatory synaptic alpha function
tau_in    ms      Rise time of the inhibitory synaptic alpha function
E_Na      mV      Sodium reversal potential
g_Na      nS      Sodium peak conductance
E_K       mV      Potassium reversal potential
g_K       nS      Potassium peak conductance
Act_m     real    Activation variable m
Inact_h   real    Inactivation variable h
Act_n     real    Activation variable n
I_e       pA      External input current
========  ======  ============================================================
 
Problems/Todo
+++++++++++++
 
- better spike detection
- initial wavelet/spike at simulation onset
 
References
++++++++++
 
 
.. footbibliography::
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, CurrentEvent, DataLoggingRequest
 
See also
++++++++
 
hh_cond_exp_traub
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: hh_psc_alpha
 
EndUserDocs */
// clang-format on
 
void register_hh_psc_alpha( const std::string& name );
 
class hh_psc_alpha : public ArchivingNode
{
 
public:
  hh_psc_alpha();
  hh_psc_alpha( const hh_psc_alpha& );
  ~hh_psc_alpha() override;
 
  using Node::handle;
  using Node::handles_test_event;
 
  size_t send_test_event( Node&, size_t, synindex, bool ) override;
 
  void handle( SpikeEvent& ) override;
  void handle( CurrentEvent& ) override;
  void handle( DataLoggingRequest& ) override;
 
  size_t handles_test_event( SpikeEvent&, size_t ) override;
  size_t handles_test_event( CurrentEvent&, size_t ) override;
  size_t handles_test_event( DataLoggingRequest&, size_t ) override;
 
  void get_status( Dictionary& ) const override;
  void set_status( const Dictionary& ) override;
 
private:
  void init_buffers_() override;
  void pre_run_hook() override;
  void update( Time const&, const long, const long ) override;
 
  // END Boilerplate function declarations ----------------------------
 
  // Friends --------------------------------------------------------
 
  // make dynamics function quasi-member
  friend int hh_psc_alpha_dynamics( double, const double*, double*, void* );
 
  // The next two classes need to be friend to access the State_ class/member
  friend class RecordablesMap< hh_psc_alpha >;
  friend class UniversalDataLogger< hh_psc_alpha >;
 
private:
  // ----------------------------------------------------------------
 
  struct Parameters_
  {
    double t_ref_;    
    double g_Na;      
    double g_K;       
    double g_L;       
    double C_m;       
    double E_Na;      
    double E_K;       
    double E_L;       
    double tau_synE;  
    double tau_synI;  
    double I_e;       
 
    Parameters_();  
 
    void get( Dictionary& ) const;              
    void set( const Dictionary&, Node* node );  
  };
 
public:
  // ----------------------------------------------------------------
 
  struct State_
  {
    enum StateVecElems
    {
      V_M = 0,
      HH_M,    // 1
      HH_H,    // 2
      HH_N,    // 3
      DI_EXC,  // 4
      I_EXC,   // 5
      DI_INH,  // 6
      I_INH,   // 7
      STATE_VEC_SIZE
    };
 
 
    double y_[ STATE_VEC_SIZE ];
    int r_;  
 
    State_( const Parameters_& );  
    State_( const State_& );
 
    State_& operator=( const State_& );
 
    void get( Dictionary& ) const;
    void set( const Dictionary&, Node* node );
  };
 
  // ----------------------------------------------------------------
 
private:
  struct Buffers_
  {
    Buffers_( hh_psc_alpha& );                   
    Buffers_( const Buffers_&, hh_psc_alpha& );  
 
    UniversalDataLogger< hh_psc_alpha > logger_;
 
    RingBuffer spike_exc_;
    RingBuffer spike_inh_;
    RingBuffer currents_;
 
    gsl_odeiv_step* s_;     
    gsl_odeiv_control* c_;  
    gsl_odeiv_evolve* e_;   
    gsl_odeiv_system sys_;  
 
    // Since IntegrationStep_ is initialized with step_, and the resolution
    // cannot change after nodes have been created, it is safe to place both
    // here.
    double step_;             
    double IntegrationStep_;  
 
    double I_stim_;
  };
 
  // ----------------------------------------------------------------
 
  struct Variables_
  {
    double PSCurrInit_E_;
 
    double PSCurrInit_I_;
 
    int RefractoryCounts_;
  };
 
  // Access functions for UniversalDataLogger -------------------------------
 
  template < State_::StateVecElems elem >
  double
  get_y_elem_() const
  {
    return S_.y_[ elem ];
  }
 
  // ----------------------------------------------------------------
 
  Parameters_ P_;
  State_ S_;
  Variables_ V_;
  Buffers_ B_;
 
  static RecordablesMap< hh_psc_alpha > recordablesMap_;
};
 
 
inline size_t
hh_psc_alpha::send_test_event( Node& target, size_t receptor_type, synindex, bool )
{
  SpikeEvent e;
  e.set_sender( *this );
 
  return target.handles_test_event( e, receptor_type );
}
 
 
inline size_t
hh_psc_alpha::handles_test_event( SpikeEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
hh_psc_alpha::handles_test_event( CurrentEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
hh_psc_alpha::handles_test_event( DataLoggingRequest& dlr, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return B_.logger_.connect_logging_device( dlr, recordablesMap_ );
}
 
inline void
hh_psc_alpha::get_status( Dictionary& d ) const
{
  P_.get( d );
  S_.get( d );
  ArchivingNode::get_status( d );
 
  d[ names::recordables ] = recordablesMap_.get_list();
}
 
inline void
hh_psc_alpha::set_status( const Dictionary& d )
{
  Parameters_ ptmp = P_;  // temporary copy in case of errors
  ptmp.set( d, this );    // throws if BadProperty
  State_ stmp = S_;       // temporary copy in case of errors
  stmp.set( d, this );    // throws if BadProperty
 
  // We now know that (ptmp, stmp) are consistent. We do not
  // write them back to (P_, S_) before we are also sure that
  // the properties to be set in the parent class are internally
  // consistent.
  ArchivingNode::set_status( d );
 
  // if we get here, temporaries contain consistent set of properties
  P_ = ptmp;
  S_ = stmp;
}
 
}  // namespace
 
#endif  // HAVE_GSL
#endif  // HH_PSC_ALPHA_H